Yes, we need to know "what" that difference in file or path pointers is before asking "why". So looking at and comparing the paths and maybe also the literal project file xml might lead to an answer.

On the surface, it's illogical for a file to save using X file paths, and then open later asking for different files ort paths, so if that's happening something is going wrong somewhere in the middle. Something is not getting saved or stored or recalled correctly for some reason.

Unless it's a thing that's only happened in one project, an anomaly, we probably need to track it down in case it happens again.

If you can save the project and then attach the *.project file. Then Save to New Folder and also attach that new *.project file so that we can compare them.

Note: This should be easier to sort with Luis acting as an intermediary where Google translate may or may not be 100% accurate.